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- Genre: Doctoral Dissertation
- Creators: Arizona State University
- Member of: ASU Electronic Theses and Dissertations
Description
Continuous monitoring in the adequate temporal and spatial scale is necessary for a better understanding of environmental variations. But field deployments of molecular biological analysis platforms in that scale are currently hindered because of issues with power, throughput and automation. Currently, such analysis is performed by the collection of large sample volumes from over a wide area and transporting them to laboratory testing facilities, which fail to provide any real-time information. This dissertation evaluates the systems currently utilized for in-situ field analyses and the issues hampering the successful deployment of such bioanalytial instruments for environmental applications. The design and development of high throughput, low power, and autonomous Polymerase Chain Reaction (PCR) instruments, amenable for portable field operations capable of providing quantitative results is presented here as part of this dissertation. A number of novel innovations have been reported here as part of this work in microfluidic design, PCR thermocycler design, optical design and systems integration. Emulsion microfluidics in conjunction with fluorinated oils and Teflon tubing have been used for the fluidic module that reduces cross-contamination eliminating the need for disposable components or constant cleaning. A cylindrical heater has been designed with the tubing wrapped around fixed temperature zones enabling continuous operation. Fluorescence excitation and detection have been achieved by using a light emitting diode (LED) as the excitation source and a photomultiplier tube (PMT) as the detector. Real-time quantitative PCR results were obtained by using multi-channel fluorescence excitation and detection using LED, optical fibers and a 64-channel multi-anode PMT for measuring continuous real-time fluorescence. The instrument was evaluated by comparing the results obtained with those obtained from a commercial instrument and found to be comparable. To further improve the design and enhance its field portability, this dissertation also presents a framework for the instrumentation necessary for a portable digital PCR platform to achieve higher throughputs with lower power. Both systems were designed such that it can easily couple with any upstream platform capable of providing nucleic acid for analysis using standard fluidic connections. Consequently, these instruments can be used not only in environmental applications, but portable diagnostics applications as well.
ContributorsRay, Tathagata (Author) / Youngbull, Cody (Thesis advisor) / Goryll, Michael (Thesis advisor) / Blain Christen, Jennifer (Committee member) / Yu, Hongyu (Committee member) / Arizona State University (Publisher)
Created2013
Description
Coronary computed tomography angiography (CTA) has a high negative predictive value for ruling out coronary artery disease with non-invasive evaluation of the coronary arteries. My work has attempted to provide metrics that could increase the positive predictive value of coronary CTA through the use of dual energy CTA imaging. After developing an algorithm for obtaining calcium scores from a CTA exam, a dual energy CTA exam was performed on patients at dose levels equivalent to levels for single energy CTA with a calcium scoring exam. Calcium Agatston scores obtained from the dual energy CTA exam were within ±11% of scores obtained with conventional calcium scoring exams. In the presence of highly attenuating coronary calcium plaques, the virtual non-calcium images obtained with dual energy CTA were able to successfully measure percent coronary stenosis within 5% of known stenosis values, which is not possible with single energy CTA images due to the presence of the calcium blooming artifact. After fabricating an anthropomorphic beating heart phantom with coronary plaques, characterization of soft plaque vulnerability to rupture or erosion was demonstrated with measurements of the distance from soft plaque to aortic ostium, percent stenosis, and percent lipid volume in soft plaque. A classification model was developed, with training data from the beating heart phantom and plaques, which utilized support vector machines to classify coronary soft plaque pixels as lipid or fibrous. Lipid versus fibrous classification with single energy CTA images exhibited a 17% error while dual energy CTA images in the classification model developed here only exhibited a 4% error. Combining the calcium blooming correction and the percent lipid volume methods developed in this work will provide physicians with metrics for increasing the positive predictive value of coronary CTA as well as expanding the use of coronary CTA to patients with highly attenuating calcium plaques.
ContributorsBoltz, Thomas (Author) / Frakes, David (Thesis advisor) / Towe, Bruce (Committee member) / Kodibagkar, Vikram (Committee member) / Pavlicek, William (Committee member) / Bouman, Charles (Committee member) / Arizona State University (Publisher)
Created2013
Description
Water resource management is becoming increasingly burdened by uncertain and fluctuating conditions resulting from climate change and population growth which place increased demands on already strained resources. Innovative water management schemes are necessary to address the reality of available water supplies. One such approach is the substitution of trade in virtual water for the use of local water supplies. This study provides a review of existing work in the use of virtual water and water footprint methods. Virtual water trade has been shown to be a successful method for addressing water scarcity and decreasing overall water consumption by shifting high water consumptive processes to wetter regions. These results however assume that all water resource supplies are equivalent regardless of physical location and they do not tie directly to economic markets. In this study we introduce a new mathematical framework, Embedded Resource Accounting (ERA), which is a synthesis of several different analytical methods presently used to quantify and describe human interactions with the economy and the natural environment. We define the specifics of the ERA framework in a generic context for the analysis of embedded resource trade in a way that links directly with the economics of that trade. Acknowledging the cyclical nature of water and the abundance of actual water resources on Earth, this study addresses fresh water availability within a given region. That is to say, the quantities of fresh water supplies annually available at acceptable quality for anthropogenic uses. The results of this research provide useful tools for water resource managers and policy makers to inform decision making on, (1) reallocation of local available fresh water resources, and (2) strategic supplementation of those resources with outside fresh water resources via the import of virtual water.
ContributorsAdams, Elizabeth Anne (Author) / Ruddell, Benjamin L (Thesis advisor) / Allenby, Braden R. (Thesis advisor) / Seager, Thomas P (Committee member) / Arizona State University (Publisher)
Created2013
Description
In a laboratory setting, the soil volume change behavior is best represented by using various testing standards on undisturbed or remolded samples. Whenever possible, it is most precise to use undisturbed samples to assess the volume change behavior but in the absence of undisturbed specimens, remodeled samples can be used. If that is the case, the soil is compacted to in-situ density and water content (or matric suction), which should best represent the expansive profile in question. It is standard practice to subject the specimen to a wetting process at a particular net normal stress. Even though currently accepted laboratory testing standard procedures provide insight on how the profile conditions changes with time, these procedures do not assess the long term effects on the soil due to climatic changes. In this experimental study, an assessment and quantification of the effect of multiple wetting/drying cycles on the volume change behavior of two different naturally occurring soils was performed. The changes in wetting and drying cycles were extreme when comparing the swings in matric suction. During the drying cycle, the expansive soil was subjected to extreme conditions, which decreased the moisture content less than the shrinkage limit. Nevertheless, both soils were remolded at five different compacted conditions and loaded to five different net normal stresses. Each sample was subjected to six wetting and drying cycles. During the assessment, it was evident from the results that the swell/collapse strain is highly non-linear at low stress levels. The strain-net normal stress relationship cannot be defined by one single function without transforming the data. Therefore, the dataset needs to be fitted to a bi-modal logarithmic function or to a logarithmic transformation of net normal stress in order to use a third order polynomial fit. It was also determined that the moisture content changes with time are best fit by non-linear functions. For the drying cycle, the radial strain was determined to have a constant rate of change with respect to the axial strain. However, for the wetting cycle, there was not enough radial strain data to develop correlations and therefore, an assumption was made based on 55 different test measurements/observations, for the wetting cycles. In general, it was observed that after each subsequent cycle, higher swelling was exhibited for lower net normal stress values; while higher collapse potential was observed for higher net normal stress values, once the net normal stress was less than/greater than a threshold net normal stress value. Furthermore, the swelling pressure underwent a reduction in all cases. Particularly, the Anthem soil exhibited a reduction in swelling pressure by at least 20 percent after the first wetting/drying cycle; while Colorado soil exhibited a reduction of 50 percent. After about the fourth cycle, the swelling pressure seemed to stabilized to an equilibrium value at which a reduction of 46 percent was observed for the Anthem soil and 68 percent reduction for the Colorado soil. The impact of the initial compacted conditions on heave characteristics was studied. Results indicated that materials compacted at higher densities exhibited greater swell potential. When comparing specimens compacted at the same density but at different moisture content (matric suction), it was observed that specimens compacted at higher suction would exhibit higher swelling potential, when subjected to the same net normal stress. The least amount of swelling strain was observed on specimens compacted at the lowest dry density and the lowest matric suction (higher water content). The results from the laboratory testing were used to develop ultimate heave profiles for both soils. This analysis showed that even though the swell pressure for each soil decreased with cycles, the amount of heave would increase or decrease depending upon the initial compaction condition. When the specimen was compacted at 110% of optimum moisture content and 90% of maximum dry density, it resulted in an ultimate heave reduction of 92 percent for Anthem and 685 percent for Colorado soil. On the other hand, when the soils were compacted at 90% optimum moisture content and 100% of the maximum dry density, Anthem specimens heave 78% more and Colorado specimens heave was reduced by 69%. Based on the results obtained, it is evident that the current methods to estimate heave and swelling pressure do not consider the effect of wetting/drying cycles; and seem to fail capturing the free swell potential of the soil. Recommendations for improvement current methods of practice are provided.
ContributorsRosenbalm, Daniel Curtis (Author) / Zapata, Claudia E (Thesis advisor) / Houston, Sandra L. (Committee member) / Kavazanjian, Edward (Committee member) / Witczak, Mathew W (Committee member) / Arizona State University (Publisher)
Created2013
Description
The efficacy of deep brain stimulation (DBS) in Parkinson's disease (PD) has been convincingly demonstrated in studies that compare motor performance with and without stimulation, but characterization of performance at intermediate stimulation amplitudes has been limited. This study investigated the effects of changing DBS amplitude in order to assess dose-response characteristics, inter-subject variability, consistency of effect across outcome measures, and day-to-day variability. Eight subjects with PD and bilateral DBS systems were evaluated at their clinically determined stimulation (CDS) and at three reduced amplitude conditions: approximately 70%, 30%, and 0% of the CDS (MOD, LOW, and OFF, respectively). Overall symptom severity and performance on a battery of motor tasks - gait, postural control, single-joint flexion-extension, postural tremor, and tapping - were assessed at each condition using the motor section of the Unified Parkinson's Disease Rating Scale (UPDRS-III) and quantitative measures. Data were analyzed to determine whether subjects demonstrated a threshold response (one decrement in stimulation resulted in ≥ 70% of the maximum change) or a graded response to reduced stimulation. Day-to-day variability was assessed using the CDS data from the three testing sessions. Although the cohort as a whole demonstrated a graded response on several measures, there was high variability across subjects, with subsets exhibiting graded, threshold, or minimal responses. Some subjects experienced greater variability in their CDS performance across the three days than the change induced by reducing stimulation. For several tasks, a subset of subjects exhibited improved performance at one or more of the reduced conditions. Reducing stimulation did not affect all subjects equally, nor did it uniformly affect each subject's performance across tasks. These results indicate that altered recruitment of neural structures can differentially affect motor capabilities and demonstrate the need for clinical consideration of the effects on multiple symptoms across several days when selecting DBS parameters.
ContributorsConovaloff, Alison (Author) / Abbas, James (Thesis advisor) / Krishnamurthi, Narayanan (Committee member) / Mahant, Padma (Committee member) / Jung, Ranu (Committee member) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2013
Description
Cancer is the second leading cause of death in the United States and novel methods of treating advanced malignancies are of high importance. Of these deaths, prostate cancer and breast cancer are the second most fatal carcinomas in men and women respectively, while pancreatic cancer is the fourth most fatal in both men and women. Developing new drugs for the treatment of cancer is both a slow and expensive process. It is estimated that it takes an average of 15 years and an expense of $800 million to bring a single new drug to the market. However, it is also estimated that nearly 40% of that cost could be avoided by finding alternative uses for drugs that have already been approved by the Food and Drug Administration (FDA). The research presented in this document describes the testing, identification, and mechanistic evaluation of novel methods for treating many human carcinomas using drugs previously approved by the FDA. A tissue culture plate-based screening of FDA approved drugs will identify compounds that can be used in combination with the protein TRAIL to induce apoptosis selectively in cancer cells. Identified leads will next be optimized using high-throughput microfluidic devices to determine the most effective treatment conditions. Finally, a rigorous mechanistic analysis will be conducted to understand how the FDA-approved drug mitoxantrone, sensitizes cancer cells to TRAIL-mediated apoptosis.
ContributorsTaylor, David (Author) / Rege, Kaushal (Thesis advisor) / Jayaraman, Arul (Committee member) / Nielsen, David (Committee member) / Kodibagkar, Vikram (Committee member) / Dai, Lenore (Committee member) / Arizona State University (Publisher)
Created2013
Description
Intracortical microstimulation (ICMS) within somatosensory cortex can produce artificial sensations including touch, pressure, and vibration. There is significant interest in using ICMS to provide sensory feedback for a prosthetic limb. In such a system, information recorded from sensors on the prosthetic would be translated into electrical stimulation and delivered directly to the brain, providing feedback about features of objects in contact with the prosthetic. To achieve this goal, multiple simultaneous streams of information will need to be encoded by ICMS in a manner that produces robust, reliable, and discriminable sensations. The first segment of this work focuses on the discriminability of sensations elicited by ICMS within somatosensory cortex. Stimulation on multiple single electrodes and near-simultaneous stimulation across multiple electrodes, driven by a multimodal tactile sensor, were both used in these experiments. A SynTouch BioTac sensor was moved across a flat surface in several directions, and a subset of the sensor's electrode impedance channels were used to drive multichannel ICMS in the somatosensory cortex of a non-human primate. The animal performed a behavioral task during this stimulation to indicate the discriminability of sensations evoked by the electrical stimulation. The animal's responses to ICMS were somewhat inconsistent across experimental sessions but indicated that discriminable sensations were evoked by both single and multichannel ICMS. The factors that affect the discriminability of stimulation-induced sensations are not well understood, in part because the relationship between ICMS and the neural activity it induces is poorly defined. The second component of this work was to develop computational models that describe the populations of neurons likely to be activated by ICMS. Models of several neurons were constructed, and their responses to ICMS were calculated. A three-dimensional cortical model was constructed using these cell models and used to identify the populations of neurons likely to be recruited by ICMS. Stimulation activated neurons in a sparse and discontinuous fashion; additionally, the type, number, and location of neurons likely to be activated by stimulation varied with electrode depth.
ContributorsOverstreet, Cynthia K (Author) / Helms Tillery, Stephen I (Thesis advisor) / Santos, Veronica (Committee member) / Buneo, Christopher (Committee member) / Otto, Kevin (Committee member) / Santello, Marco (Committee member) / Arizona State University (Publisher)
Created2013
Description
This research is focused on two separate but related topics. The first uses an electroencephalographic (EEG) brain-computer interface (BCI) to explore the phenomenon of motor learning transfer. The second takes a closer look at the EEG-BCI itself and tests an alternate way of mapping EEG signals into machine commands. We test whether motor learning transfer is more related to use of shared neural structures between imagery and motor execution or to more generalized cognitive factors. Using an EEG-BCI, we train one group of participants to control the movements of a cursor using embodied motor imagery. A second group is trained to control the cursor using abstract motor imagery. A third control group practices moving the cursor using an arm and finger on a touch screen. We hypothesized that if motor learning transfer is related to the use of shared neural structures then the embodied motor imagery group would show more learning transfer than the abstract imaging group. If, on the other hand, motor learning transfer results from more general cognitive processes, then the abstract motor imagery group should also demonstrate motor learning transfer to the manual performance of the same task. Our findings support that motor learning transfer is due to the use of shared neural structures between imaging and motor execution of a task. The abstract group showed no motor learning transfer despite being better at EEG-BCI control than the embodied group. The fact that more participants were able to learn EEG-BCI control using abstract imagery suggests that abstract imagery may be more suitable for EEG-BCIs for some disabilities, while embodied imagery may be more suitable for others. In Part 2, EEG data collected in the above experiment was used to train an artificial neural network (ANN) to map EEG signals to machine commands. We found that our open-source ANN using spectrograms generated from SFFTs is fundamentally different and in some ways superior to Emotiv's proprietary method. Our use of novel combinations of existing technologies along with abstract and embodied imagery facilitates adaptive customization of EEG-BCI control to meet needs of individual users.
Contributorsda Silva, Flavio J. K (Author) / Mcbeath, Michael K (Thesis advisor) / Helms Tillery, Stephen (Committee member) / Presson, Clark (Committee member) / Sugar, Thomas (Committee member) / Arizona State University (Publisher)
Created2013
Description
Electrical neural activity detection and tracking have many applications in medical research and brain computer interface technologies. In this thesis, we focus on the development of advanced signal processing algorithms to track neural activity and on the mapping of these algorithms onto hardware to enable real-time tracking. At the heart of these algorithms is particle filtering (PF), a sequential Monte Carlo technique used to estimate the unknown parameters of dynamic systems. First, we analyze the bottlenecks in existing PF algorithms, and we propose a new parallel PF (PPF) algorithm based on the independent Metropolis-Hastings (IMH) algorithm. We show that the proposed PPF-IMH algorithm improves the root mean-squared error (RMSE) estimation performance, and we demonstrate that a parallel implementation of the algorithm results in significant reduction in inter-processor communication. We apply our implementation on a Xilinx Virtex-5 field programmable gate array (FPGA) platform to demonstrate that, for a one-dimensional problem, the PPF-IMH architecture with four processing elements and 1,000 particles can process input samples at 170 kHz by using less than 5% FPGA resources. We also apply the proposed PPF-IMH to waveform-agile sensing to achieve real-time tracking of dynamic targets with high RMSE tracking performance. We next integrate the PPF-IMH algorithm to track the dynamic parameters in neural sensing when the number of neural dipole sources is known. We analyze the computational complexity of a PF based method and propose the use of multiple particle filtering (MPF) to reduce the complexity. We demonstrate the improved performance of MPF using numerical simulations with both synthetic and real data. We also propose an FPGA implementation of the MPF algorithm and show that the implementation supports real-time tracking. For the more realistic scenario of automatically estimating an unknown number of time-varying neural dipole sources, we propose a new approach based on the probability hypothesis density filtering (PHDF) algorithm. The PHDF is implemented using particle filtering (PF-PHDF), and it is applied in a closed-loop to first estimate the number of dipole sources and then their corresponding amplitude, location and orientation parameters. We demonstrate the improved tracking performance of the proposed PF-PHDF algorithm and map it onto a Xilinx Virtex-5 FPGA platform to show its real-time implementation potential. Finally, we propose the use of sensor scheduling and compressive sensing techniques to reduce the number of active sensors, and thus overall power consumption, of electroencephalography (EEG) systems. We propose an efficient sensor scheduling algorithm which adaptively configures EEG sensors at each measurement time interval to reduce the number of sensors needed for accurate tracking. We combine the sensor scheduling method with PF-PHDF and implement the system on an FPGA platform to achieve real-time tracking. We also investigate the sparsity of EEG signals and integrate compressive sensing with PF to estimate neural activity. Simulation results show that both sensor scheduling and compressive sensing based methods achieve comparable tracking performance with significantly reduced number of sensors.
ContributorsMiao, Lifeng (Author) / Chakrabarti, Chaitali (Thesis advisor) / Papandreou-Suppappola, Antonia (Thesis advisor) / Zhang, Junshan (Committee member) / Bliss, Daniel (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Unsaturated soil mechanics is becoming a part of geotechnical engineering practice, particularly in applications to moisture sensitive soils such as expansive and collapsible soils and in geoenvironmental applications. The soil water characteristic curve, which describes the amount of water in a soil versus soil suction, is perhaps the most important soil property function for application of unsaturated soil mechanics. The soil water characteristic curve has been used extensively for estimating unsaturated soil properties, and a number of fitting equations for development of soil water characteristic curves from laboratory data have been proposed by researchers. Although not always mentioned, the underlying assumption of soil water characteristic curve fitting equations is that the soil is sufficiently stiff so that there is no change in total volume of the soil while measuring the soil water characteristic curve in the laboratory, and researchers rarely take volume change of soils into account when generating or using the soil water characteristic curve. Further, there has been little attention to the applied net normal stress during laboratory soil water characteristic curve measurement, and often zero to only token net normal stress is applied. The applied net normal stress also affects the volume change of the specimen during soil suction change. When a soil changes volume in response to suction change, failure to consider the volume change of the soil leads to errors in the estimated air-entry value and the slope of the soil water characteristic curve between the air-entry value and the residual moisture state. Inaccuracies in the soil water characteristic curve may lead to inaccuracies in estimated soil property functions such as unsaturated hydraulic conductivity. A number of researchers have recently recognized the importance of considering soil volume change in soil water characteristic curves. The study of correct methods of soil water characteristic curve measurement and determination considering soil volume change, and impacts on the unsaturated hydraulic conductivity function was of the primary focus of this study. Emphasis was placed upon study of the effect of volume change consideration on soil water characteristic curves, for expansive clays and other high volume change soils. The research involved extensive literature review and laboratory soil water characteristic curve testing on expansive soils. The effect of the initial state of the specimen (i.e. slurry versus compacted) on soil water characteristic curves, with regard to volume change effects, and effect of net normal stress on volume change for determination of these curves, was studied for expansive clays. Hysteresis effects were included in laboratory measurements of soil water characteristic curves as both wetting and drying paths were used. Impacts of soil water characteristic curve volume change considerations on fluid flow computations and associated suction-change induced soil deformations were studied through numerical simulations. The study includes both coupled and uncoupled flow and stress-deformation analyses, demonstrating that the impact of volume change consideration on the soil water characteristic curve and the estimated unsaturated hydraulic conductivity function can be quite substantial for high volume change soils.
ContributorsBani Hashem, Elham (Author) / Houston, Sandra L. (Thesis advisor) / Kavazanjian, Edward (Committee member) / Zapata, Claudia (Committee member) / Arizona State University (Publisher)
Created2013